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In this paper, we have demonstrated that a three-dimensional (3-D) miniaturized rectangular cavity resonator (MRCR) with simultaneously shorten electric length and electric width can be designed, fabricated and tested through extending the analysis of the metamaterial-based cavity resonator to the 3-D case. Resonance equation solutions of a rectangular cavity resonator filled with anisotropic metamaterials bilayer are explored. Results show that the resonance frequency of such a cavity resonator can be simultaneously independent on the cavity width and length when the transversal components of the permeability tensors of the filled metamaterials have opposite sign. Based on the results, a 3-D MRCR is designed, fabricated, and tested by using modified SRRs with negative transversal permeability. It is shown that the electrical length and width of the designed 3-D MRCR are simultaneously reduced to 0.2 much smaller than 0.5, which is the theoretical minimum of the electric length and width of a conventional rectangular cavity resonator.